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General Function Checklist


  1. Download and

...

  1. unzip the following folder: test genomes.zip 
  2. The folder "test genomes" should contain the following files:
    1. E_unicornis_Jul_2043.bed.gz.tbi
    2. E_unicornis_Jul_2043.bed.gz
    3. E_unicornis_Jul_2043.2bit
    4. T_rex_Jun_1993.2bit
  3. Start IGB 9.1.8 or later.
  4. Select the Plug-ins tab.
  5. Click Launch App Manager.

...

  1. Select Manage Repositories...

...

  1. Click Add...

      In the Add Plugin Repository window enter the following information:

        1. Name: Quickload Saver Repo
        2. URL: https://bitbucket.org/lorainelab/quickload-saver/downloads/
      1. Click Submit.
      2. Click Done.

      In the Preferences window App Repositories tab:
      Click Done

      Image Removed

      In the IGB App Manager window:Image Added

      • Checkpoint:
      •  mac
      •  linux
      •  windows


      1. In the Plug-ins tab, click Launch App Manager.
      2. Select the Quickload Saver app.
      3. Click Install.

      Image Added

      • Checkpoint:
      •  mac
      •  linux
      •  windows

      Image Removed

      1. Close the IGB App Manager window.

      ...

      1. Select File > Open Genome from File...

      ...

        1. Reference Sequence: Click Choose File... and select E_unicornis_Jul_2043.2bit
        2. Genus: Equus
        3. Species: unicornis
        4. Variety: (leave blank)
        5. Genome release date: July 2043
      1. Click OK.
      2. Select File > Open File...
      3. Select E_unicornis_Jul_2043.bed.gz
      4. Click Open.
      5. In the Data Access tab

      ...

      1. at the bottom of IGB,
        1. Change the Load Mode to Genome for E_unicornis_Jul_2043.bed.gz
        2. Change the color of the foreground (FG) to red.

      • Checkpoint:
      •  mac
      •  linux
      •  windows


      1. Select File > Save Custom Genome to Local Quickload Site
      2. Select your desktop as the destination and unicorn as the name.
      3. Click Save

      ...

      1. .
      2. Select File > Open Genome from File...

      ...

        1. Reference Sequence: Click Choose File... and select the T_rex_Jun_1993.2bit
        2. Genus: Tyrannosaurus 
        3. Species: rex
        4. Variety: (leave blank)
        5. Genome release date:

      ...

        1. June 1993
      1. Click OK.
      2. Select File > Open URL...

      ...

      1. Enter URL: http://igbquickload.org/quickload/S_cerevisiae_Apr_2011/S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz

      ...

      1. Click OK.

      In IGBImage Added

      • Checkpoint:
      •  mac
      •  linux
      •  windows


      In the Data Access tab in the Data Management Table sectionat the bottom of IGB:

      • Change the Load Mode to Genome for S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz
      • Change the color of the foreground (FG) to green.

      • Checkpoint:
      •  mac
      •  linux
      •  windows


      1. Select File > Save Custom Genome to Local Quickload Site.
      2. Select your desktop as the destination and rex as the name.

      In IGB:

      1. Select File > Preferences...
      2. In the Preferences window select the Other Options tab.
      3. Click Reset Preference to Defaults and then click Yes

      ...

      1. . IGB will close.

      ...

      1. Start IGB

      ...

      1. .
      2. Select File > Preferences

      ...

      1. .
      2. Select the Data Sources tab.

      ...

      1. Click Add...

      ...

        1. Name: unicorn
        2. Type: Quickload
        3. Click Choose local folder
      1. Select the unicorn folder on your desktop and click Open.

      Image Removed

      1. Click Submit

      In the Data Sources tab:Image Added

      • Checkpoint:
      •  mac
      •  linux
      •  windows


      1. Click Add...

      ...


        1. Name: rex
        2. Type: Quickload
      1. Click Choose local folder.
      2. Select the rex folder on your desktop and click Open.
      3. Click Submit.

      In the Add Data Source tab:
      Click Submit

      Image Added

      • Checkpoint:
      •  mac
      •  linux
      •  windows

      Image Removed

      1. Close the Preferences window.

      ...

      1. Select the Log tab and click Clear.

      ...

      1. Open the E_unicornis_Jul_

      ...

      1. 2043 genome.
      2. In the Data Access tab, E_unicornis_Jul_2043.bed.gz should be set to Load Mode Genome and should be red (FG).

      Image AddedCompare your

      • Your IGB appears to

      ...

      • look the same as the above image.
      •  mac
      •  linux
      •  windows

      Image Removed


      1. Navigate to: chrXVI:2,618-2,661
      2. Click Load Sequence.

      Image AddedCompare your

      • Your IGB appears to

      ...

      • look the same as the above image.
      •  mac
      •  linux
      •  windows

      Image Removed


      Select the Log tab and check for errors.No

      • There are no errors in the Log

      ...

      • .
      •  mac
      •  linux
      •  windows


      1. Click Clear in the Log tab

      ...

      1. .

      ...

      1. Open the T_rex_Jun_

      ...

      1. 1993 genome.
      2. In the Data Access tab, S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz should be set to Load Mode Genome and should be green (FG).

      Compare your Image Added

      • Your IGB appears to

      ...

      • look the same as the above image.
      •  mac
      •  linux
      •  windows

      Image Removed


      1. Navigate to: chrXVI:2,618-2,661
      2. Click Load Sequence.

      Compare your Image Added

      • Your IGB appears to

      ...

      • look the same as the above image.
      •  mac
      •  linux
      •  windows

      Image Removed


      1. Select the Log tab and check for errors.
      2. Click Clear in the Log tab

      ...

      1. .
      • There are no errors

      ...

      • in the Log

      ...

      • .
      •  mac
      •  linux
      •  windows